Starting phenix.real_space_refine
on Wed Sep 17 21:39:43 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2025/6pwe_20506.map"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      14      5.16       5
     C    6576      2.51       5
     N    2231      2.21       5
     O    2808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11923
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 626
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 789
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 743
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Restraints were copied for chains:
    E, F, G, H
  Time building chain proxies: 2.75, per 1000 atoms: 0.23
  Number of scatterers: 11923
  At special positions: 0
  Unit cell: (108.36, 113.4, 120.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     294     15.00
     O    2808      8.00
     N    2231      7.00
     C    6576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 239.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      59.4% alpha, 1.6% beta
      95 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
    Processing helix  chain 'A' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 105
      removed outlier: 3.841A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 3.602A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 128
      removed outlier: 3.589A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 39
      removed outlier: 3.533A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.853A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.699A  pdb=" N   ALA C  20 " --> pdb=" O   ARG C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU C  32 " --> pdb=" O   ARG C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 3.700A  pdb=" N   ALA C  51 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU C  63 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN C  67 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA C  68 " --> pdb=" O   LEU C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU C  82 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN C  83 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS C  94 " --> pdb=" O   GLU C  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 43
      removed outlier: 3.690A  pdb=" N   ILE D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS D  40 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS D  43 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN D  60 " --> pdb=" O   MET D  56 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ALA D  72 " --> pdb=" O   GLU D  68 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR D  80 " --> pdb=" O   ARG D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LYS D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 50
    Processing helix  chain 'E' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU E  70 " --> pdb=" O   PRO E  66 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 105
      removed outlier: 3.842A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN E  93 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU E  94 " --> pdb=" O   MET E  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 113
      removed outlier: 3.601A  pdb=" N   HIS E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 128
      removed outlier: 3.590A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 39
      removed outlier: 3.534A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.854A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.698A  pdb=" N   ALA G  20 " --> pdb=" O   ARG G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU G  32 " --> pdb=" O   ARG G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 3.701A  pdb=" N   ALA G  51 " --> pdb=" O   PRO G  47 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL G  53 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU G  63 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY G  66 " --> pdb=" O   LEU G  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN G  67 " --> pdb=" O   GLU G  63 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA G  68 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU G  82 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLN G  83 " --> pdb=" O   PRO G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS G  94 " --> pdb=" O   GLU G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 43
      removed outlier: 3.689A  pdb=" N   ILE H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS H  40 " --> pdb=" O   ILE H  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS H  43 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN H  60 " --> pdb=" O   MET H  56 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ALA H  72 " --> pdb=" O   GLU H  68 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG H  76 " --> pdb=" O   ALA H  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR H  80 " --> pdb=" O   ARG H  76 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER H 109 " --> pdb=" O   LYS H 105 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LYS H 113 " --> pdb=" O   SER H 109 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.787A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42
      removed outlier: 7.109A  pdb=" N   ARG C  41 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.536A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42
      removed outlier: 7.395A  pdb=" N   ARG G  41 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77

    206 hydrogen bonds defined for protein.
    600 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      225 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      95 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.30 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.32: 1843
        1.32 -     1.44: 4466
        1.44 -     1.56: 5815
        1.56 -     1.68: 586
        1.68 -     1.80: 26
  Bond restraints: 12736
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.482 -0.060 3.00e-02 1.11e+03 3.98e+00
  bond pdb=" CB  PRO A  66 "
       pdb=" CG  PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.09e+00
  bond pdb=" CB  PRO E  66 "
       pdb=" CG  PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.06e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C3'  DG I  38 "
       pdb=" O3'  DG I  38 "
    ideal  model  delta    sigma   weight residual
    1.422  1.373  0.049 3.00e-02 1.11e+03 2.68e+00
  ... (remaining 12731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 17147
        1.74 -     3.49: 1166
        3.49 -     5.23: 120
        5.23 -     6.97: 16
        6.97 -     8.71: 12
  Bond angle restraints: 18461
  Sorted by residual:
  angle pdb=" C   ARG H  30 "
        pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C   ARG D  30 "
        pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.24   -8.70 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
        pdb=" CB  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.07   -6.58 1.69e+00 3.50e-01 1.52e+01
  angle pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
        pdb=" CB  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.03   -6.54 1.69e+00 3.50e-01 1.50e+01
  angle pdb=" C   ALA C 102 "
        pdb=" N   GLN C 103 "
        pdb=" CA  GLN C 103 "
      ideal   model   delta    sigma   weight residual
     122.46  127.42   -4.96 1.41e+00 5.03e-01 1.24e+01
  ... (remaining 18456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.76: 5440
       31.76 -    63.52: 1415
       63.52 -    95.29: 44
       95.29 -   127.05: 0
      127.05 -   158.81: 3
  Dihedral angle restraints: 6902
    sinusoidal: 4744
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  LYS D  29 "
           pdb=" C   LYS D  29 "
           pdb=" N   ARG D  30 "
           pdb=" CA  ARG D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.05  -52.95     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  LYS H  29 "
           pdb=" C   LYS H  29 "
           pdb=" N   ARG H  30 "
           pdb=" CA  ARG H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.10  -52.90     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  ARG D  30 "
           pdb=" C   ARG D  30 "
           pdb=" N   LYS D  31 "
           pdb=" CA  LYS D  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.19   39.81     0      5.00e+00 4.00e-02 6.34e+01
  ... (remaining 6899 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1265
       0.044 -    0.088: 667
       0.088 -    0.133: 129
       0.133 -    0.177: 27
       0.177 -    0.221: 10
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CB  VAL G 106 "
            pdb=" CA  VAL G 106 "
            pdb=" CG1 VAL G 106 "
            pdb=" CG2 VAL G 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  VAL C 106 "
            pdb=" CA  VAL C 106 "
            pdb=" CG1 VAL C 106 "
            pdb=" CG2 VAL C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  VAL C  99 "
            pdb=" CA  VAL C  99 "
            pdb=" CG1 VAL C  99 "
            pdb=" CG2 VAL C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 1318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "   -0.046 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A  66 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  65 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO E  66 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E  66 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E  66 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H 101 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   GLY H 101 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLY H 101 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU H 102 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1315 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2734
        2.79 -     3.32: 10074
        3.32 -     3.85: 22518
        3.85 -     4.37: 26262
        4.37 -     4.90: 37230
  Nonbonded interactions: 98818
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OH  TYR H  37 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   TYR F  51 "
            pdb=" NH1 ARG F  55 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   TYR B  51 "
            pdb=" NH1 ARG B  55 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N2   DG I  21 "
            pdb=" O2   DC J -21 "
     model   vdw
     2.330 2.496
  ... (remaining 98813 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.088  12736  Z= 0.416
  Angle     :  0.929   8.715  18461  Z= 0.526
  Chirality :  0.053   0.221   2098
  Planarity :  0.007   0.069   1318
  Dihedral  : 27.121 158.809   5510
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.42 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.65 (0.18), residues: 728
  helix: -4.66 (0.11), residues: 440
  sheet:  None (None), residues: 0
  loop : -3.73 (0.27), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  30 
 TYR   0.018   0.004   TYR F  51 
 PHE   0.019   0.003   PHE A 104 
 HIS   0.008   0.002   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00952 (12736)
  covalent geometry    : angle       0.92883 (18461)
  hydrogen bonds       : bond        0.31222 (  431)
  hydrogen bonds       : angle      11.97429 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7194 (tt0) cc_final: 0.6709 (tp30)
REVERT: B   31 LYS cc_start: 0.8599 (tttt) cc_final: 0.8096 (mptt)
REVERT: B   51 TYR cc_start: 0.8455 (m-80) cc_final: 0.7978 (m-80)
REVERT: B   79 LYS cc_start: 0.7955 (mttp) cc_final: 0.7747 (mtpt)
REVERT: C  109 ASN cc_start: 0.7057 (t0) cc_final: 0.6807 (m-40)
REVERT: D   48 ASP cc_start: 0.8152 (p0) cc_final: 0.7794 (p0)
REVERT: D  106 HIS cc_start: 0.7772 (m90) cc_final: 0.7565 (m-70)
REVERT: E   41 TYR cc_start: 0.8455 (m-80) cc_final: 0.8156 (m-80)
REVERT: E   49 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7270 (tpp-160)
REVERT: E  118 THR cc_start: 0.9373 (m) cc_final: 0.9071 (p)
REVERT: F   80 THR cc_start: 0.8638 (m) cc_final: 0.8278 (p)
REVERT: F   84 MET cc_start: 0.6704 (mmm) cc_final: 0.6013 (mmm)
REVERT: F   88 TYR cc_start: 0.8433 (m-10) cc_final: 0.7793 (m-80)
REVERT: F   98 TYR cc_start: 0.8948 (m-10) cc_final: 0.8633 (m-10)
REVERT: H   40 LYS cc_start: 0.9155 (mttt) cc_final: 0.8815 (mtpt)
REVERT: H   80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7496 (m-10)
REVERT: H   97 LEU cc_start: 0.8873 (mt) cc_final: 0.8648 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1831
  time to fit residues: 59.8164
Evaluate side-chains
  171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  23 GLN
D  60 ASN
D  64 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  23 GLN
G  88 ASN
H  60 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.132657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.109675 restraints weight = 23725.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.111504 restraints weight = 13939.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112717 restraints weight = 9946.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.113384 restraints weight = 8155.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.113866 restraints weight = 7336.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12736  Z= 0.175
  Angle     :  0.637   5.663  18461  Z= 0.379
  Chirality :  0.037   0.182   2098
  Planarity :  0.005   0.048   1318
  Dihedral  : 30.759 158.996   4040
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.67 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.40 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.96 (0.23), residues: 728
  helix: -3.13 (0.18), residues: 458
  sheet:  None (None), residues: 0
  loop : -3.32 (0.29), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  96 
 TYR   0.014   0.001   TYR C  56 
 PHE   0.012   0.001   PHE E 104 
 HIS   0.004   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12736)
  covalent geometry    : angle       0.63740 (18461)
  hydrogen bonds       : bond        0.06669 (  431)
  hydrogen bonds       : angle       3.49268 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 207
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.9092 (m-80) cc_final: 0.8858 (m-80)
REVERT: A   73 GLU cc_start: 0.7216 (tt0) cc_final: 0.6940 (tp30)
REVERT: B   31 LYS cc_start: 0.8865 (tttt) cc_final: 0.8352 (mptt)
REVERT: B   59 LYS cc_start: 0.8392 (tttt) cc_final: 0.8103 (tttt)
REVERT: B   82 THR cc_start: 0.8563 (t) cc_final: 0.8096 (m)
REVERT: B   88 TYR cc_start: 0.8296 (m-80) cc_final: 0.7593 (m-10)
REVERT: C   54 MET cc_start: 0.6746 (mtp) cc_final: 0.6409 (mtm)
REVERT: C  109 ASN cc_start: 0.7195 (t0) cc_final: 0.6830 (m-40)
REVERT: D   48 ASP cc_start: 0.8006 (p0) cc_final: 0.7613 (p0)
REVERT: F   29 ILE cc_start: 0.8906 (mt) cc_final: 0.8663 (mt)
REVERT: F   55 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8319 (mtt90)
REVERT: F   84 MET cc_start: 0.6372 (mmm) cc_final: 0.4897 (tpp)
REVERT: F   88 TYR cc_start: 0.8289 (m-10) cc_final: 0.7610 (m-80)
REVERT: H   39 TYR cc_start: 0.7858 (t80) cc_final: 0.7553 (t80)
REVERT: H   40 LYS cc_start: 0.9072 (mttt) cc_final: 0.8350 (mtpt)
REVERT: H   65 ASP cc_start: 0.8578 (t70) cc_final: 0.8255 (t0)
REVERT: H   80 TYR cc_start: 0.8062 (m-10) cc_final: 0.7592 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 211
  average time/residue: 0.1348
  time to fit residues: 38.1385
Evaluate side-chains
  165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 161
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain E residue   96 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 97 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  81 HIS
C  93 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN
H  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.131118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107935 restraints weight = 24311.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.109713 restraints weight = 14527.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.110901 restraints weight = 10488.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.111596 restraints weight = 8634.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.111995 restraints weight = 7738.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12736  Z= 0.190
  Angle     :  0.607   6.571  18461  Z= 0.357
  Chirality :  0.036   0.172   2098
  Planarity :  0.005   0.044   1318
  Dihedral  : 30.573 161.403   4040
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.15 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.87 (0.27), residues: 728
  helix: -2.26 (0.21), residues: 468
  sheet:  None (None), residues: 0
  loop : -2.88 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  55 
 TYR   0.016   0.002   TYR D 118 
 PHE   0.014   0.001   PHE H  62 
 HIS   0.004   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (12736)
  covalent geometry    : angle       0.60725 (18461)
  hydrogen bonds       : bond        0.05985 (  431)
  hydrogen bonds       : angle       3.09329 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 177
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.7954 (mtp85)
REVERT: A   73 GLU cc_start: 0.7367 (tt0) cc_final: 0.6883 (tp30)
REVERT: B   31 LYS cc_start: 0.8727 (tttt) cc_final: 0.8290 (mptt)
REVERT: B   59 LYS cc_start: 0.8508 (tttt) cc_final: 0.8281 (tttt)
REVERT: B   82 THR cc_start: 0.8597 (t) cc_final: 0.8199 (m)
REVERT: B   88 TYR cc_start: 0.8163 (m-10) cc_final: 0.7521 (m-10)
REVERT: D   48 ASP cc_start: 0.8096 (p0) cc_final: 0.7768 (p0)
REVERT: E   42 ARG cc_start: 0.8211 (mtp-110) cc_final: 0.7957 (mtp180)
REVERT: E   49 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6478 (tpm170)
REVERT: F   51 TYR cc_start: 0.8730 (m-10) cc_final: 0.8398 (m-10)
REVERT: F   84 MET cc_start: 0.6455 (mmm) cc_final: 0.5333 (tpp)
REVERT: F   88 TYR cc_start: 0.8319 (m-10) cc_final: 0.7663 (m-80)
REVERT: F   98 TYR cc_start: 0.9165 (m-10) cc_final: 0.8934 (m-80)
REVERT: H   39 TYR cc_start: 0.7898 (t80) cc_final: 0.7397 (t80)
REVERT: H   54 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8435 (tptm)
REVERT: H   56 MET cc_start: 0.7806 (mmm) cc_final: 0.6767 (mtt)
REVERT: H   66 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9169 (tp)
REVERT: H   80 TYR cc_start: 0.8141 (m-10) cc_final: 0.7692 (m-10)
REVERT: H   98 LEU cc_start: 0.8456 (mp) cc_final: 0.8055 (mp)
  outliers start: 24
  outliers final: 12
  residues processed: 194
  average time/residue: 0.1335
  time to fit residues: 34.9491
Evaluate side-chains
  175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain H residue   66 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 85 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 35 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   overall best weight:    3.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
G  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.127309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.103669 restraints weight = 24560.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.105371 restraints weight = 15123.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.106463 restraints weight = 11106.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.107138 restraints weight = 9258.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.107404 restraints weight = 8335.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  12736  Z= 0.286
  Angle     :  0.706   6.837  18461  Z= 0.403
  Chirality :  0.041   0.176   2098
  Planarity :  0.005   0.050   1318
  Dihedral  : 30.917 163.639   4040
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.32 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 18.28 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.28), residues: 728
  helix: -2.09 (0.22), residues: 448
  sheet:  None (None), residues: 0
  loop : -2.63 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  89 
 TYR   0.021   0.003   TYR D 118 
 PHE   0.012   0.002   PHE E 104 
 HIS   0.007   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 (12736)
  covalent geometry    : angle       0.70598 (18461)
  hydrogen bonds       : bond        0.07048 (  431)
  hydrogen bonds       : angle       3.42460 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.7812 (mtp85)
REVERT: A   73 GLU cc_start: 0.7395 (tt0) cc_final: 0.6909 (tp30)
REVERT: B   31 LYS cc_start: 0.8785 (tttt) cc_final: 0.8290 (mptt)
REVERT: B   82 THR cc_start: 0.8493 (t) cc_final: 0.8170 (m)
REVERT: B   88 TYR cc_start: 0.8128 (m-10) cc_final: 0.7347 (m-10)
REVERT: C  101 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8739 (mp)
REVERT: D   48 ASP cc_start: 0.8226 (p0) cc_final: 0.7917 (p0)
REVERT: H   66 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9233 (tp)
  outliers start: 38
  outliers final: 26
  residues processed: 191
  average time/residue: 0.1313
  time to fit residues: 33.9192
Evaluate side-chains
  182 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue  121 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 83 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0370
   chunk 46 optimal weight:    0.9980
   chunk 86 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.5238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN
F  75 HIS
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.134378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.110743 restraints weight = 24069.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.112575 restraints weight = 14294.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.113753 restraints weight = 10298.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.114451 restraints weight = 8521.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114850 restraints weight = 7666.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12736  Z= 0.147
  Angle     :  0.567   8.025  18461  Z= 0.335
  Chirality :  0.033   0.145   2098
  Planarity :  0.004   0.051   1318
  Dihedral  : 30.203 159.631   4040
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.43 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.68 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.30), residues: 728
  helix: -1.48 (0.23), residues: 472
  sheet:  None (None), residues: 0
  loop : -2.27 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  76 
 TYR   0.047   0.002   TYR F  88 
 PHE   0.006   0.001   PHE H  62 
 HIS   0.002   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (12736)
  covalent geometry    : angle       0.56729 (18461)
  hydrogen bonds       : bond        0.05482 (  431)
  hydrogen bonds       : angle       2.61945 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7225 (tt0) cc_final: 0.6737 (tp30)
REVERT: B   25 ASN cc_start: 0.7568 (m-40) cc_final: 0.7189 (m-40)
REVERT: B   31 LYS cc_start: 0.8652 (tttt) cc_final: 0.8219 (mptt)
REVERT: B   82 THR cc_start: 0.8413 (t) cc_final: 0.8106 (m)
REVERT: B   88 TYR cc_start: 0.7800 (m-10) cc_final: 0.7400 (m-10)
REVERT: C   49 TYR cc_start: 0.8513 (t80) cc_final: 0.7965 (t80)
REVERT: D   48 ASP cc_start: 0.8031 (p0) cc_final: 0.7735 (p0)
REVERT: E   42 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7982 (ttp80)
REVERT: F   25 ASN cc_start: 0.7646 (m-40) cc_final: 0.7339 (t0)
REVERT: F   88 TYR cc_start: 0.8367 (m-80) cc_final: 0.8139 (m-80)
REVERT: F   98 TYR cc_start: 0.9243 (m-10) cc_final: 0.9005 (m-80)
REVERT: H   39 TYR cc_start: 0.7770 (t80) cc_final: 0.7374 (t80)
REVERT: H   56 MET cc_start: 0.7709 (mmm) cc_final: 0.6733 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 181
  average time/residue: 0.1403
  time to fit residues: 33.9830
Evaluate side-chains
  162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   chunk 91 optimal weight:    8.9990
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  83 GLN
C  93 ASN
G 103 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.102143 restraints weight = 24938.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103741 restraints weight = 15656.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.104794 restraints weight = 11714.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.105421 restraints weight = 9862.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.105752 restraints weight = 8960.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100  12736  Z= 0.337
  Angle     :  0.750  11.599  18461  Z= 0.422
  Chirality :  0.043   0.170   2098
  Planarity :  0.005   0.052   1318
  Dihedral  : 30.946 162.554   4040
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 20.55 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.29), residues: 728
  helix: -1.62 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -2.46 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  35 
 TYR   0.026   0.003   TYR F  88 
 PHE   0.012   0.002   PHE H  62 
 HIS   0.008   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00774 (12736)
  covalent geometry    : angle       0.75023 (18461)
  hydrogen bonds       : bond        0.07330 (  431)
  hydrogen bonds       : angle       3.49805 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.7781 (mtp85)
REVERT: A   73 GLU cc_start: 0.7238 (tt0) cc_final: 0.6915 (tp30)
REVERT: B   31 LYS cc_start: 0.8738 (tttt) cc_final: 0.8322 (mptt)
REVERT: B   82 THR cc_start: 0.8542 (t) cc_final: 0.8233 (m)
REVERT: B   88 TYR cc_start: 0.8056 (m-10) cc_final: 0.7409 (m-10)
REVERT: D   48 ASP cc_start: 0.8263 (p0) cc_final: 0.7988 (p0)
REVERT: E   42 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.8122 (ttp80)
REVERT: E   49 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6142 (tpm170)
REVERT: F   88 TYR cc_start: 0.8553 (m-80) cc_final: 0.8209 (m-80)
REVERT: H   37 TYR cc_start: 0.8551 (m-80) cc_final: 0.8219 (m-10)
REVERT: H   66 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9194 (tp)
  outliers start: 42
  outliers final: 34
  residues processed: 183
  average time/residue: 0.1302
  time to fit residues: 32.4384
Evaluate side-chains
  188 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
C  83 GLN
C  93 ASN
F  25 ASN
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.109554 restraints weight = 24203.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111371 restraints weight = 14549.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.112540 restraints weight = 10585.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.113227 restraints weight = 8798.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.113637 restraints weight = 7937.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12736  Z= 0.154
  Angle     :  0.589  10.000  18461  Z= 0.343
  Chirality :  0.034   0.161   2098
  Planarity :  0.004   0.053   1318
  Dihedral  : 30.261 158.921   4040
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 25.08 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.30), residues: 728
  helix: -0.99 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -2.18 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  76 
 TYR   0.034   0.002   TYR F  88 
 PHE   0.006   0.001   PHE G  24 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12736)
  covalent geometry    : angle       0.58887 (18461)
  hydrogen bonds       : bond        0.05530 (  431)
  hydrogen bonds       : angle       2.65367 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.8506 (tttt) cc_final: 0.8302 (mptt)
REVERT: B   59 LYS cc_start: 0.8428 (tttt) cc_final: 0.8215 (tptm)
REVERT: B   72 TYR cc_start: 0.8789 (m-80) cc_final: 0.8507 (m-80)
REVERT: B   82 THR cc_start: 0.8486 (t) cc_final: 0.8136 (m)
REVERT: B   88 TYR cc_start: 0.7744 (m-10) cc_final: 0.7291 (m-10)
REVERT: D   48 ASP cc_start: 0.8047 (p0) cc_final: 0.7744 (p0)
REVERT: D   77 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8457 (tp)
REVERT: F   27 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7529 (mm-40)
REVERT: F   98 TYR cc_start: 0.9273 (m-10) cc_final: 0.9027 (m-80)
REVERT: H   39 TYR cc_start: 0.7810 (t80) cc_final: 0.7478 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 173
  average time/residue: 0.1330
  time to fit residues: 30.7064
Evaluate side-chains
  170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 86 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN
G  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.132390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.108726 restraints weight = 24201.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.110494 restraints weight = 14571.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111633 restraints weight = 10586.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.112342 restraints weight = 8797.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.112715 restraints weight = 7938.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12736  Z= 0.168
  Angle     :  0.592   9.679  18461  Z= 0.344
  Chirality :  0.034   0.145   2098
  Planarity :  0.004   0.051   1318
  Dihedral  : 30.320 159.128   4040
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.89 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.30), residues: 728
  helix: -0.69 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -2.10 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  76 
 TYR   0.065   0.002   TYR F  88 
 PHE   0.006   0.001   PHE E 104 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12736)
  covalent geometry    : angle       0.59246 (18461)
  hydrogen bonds       : bond        0.05578 (  431)
  hydrogen bonds       : angle       2.69322 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.8506 (tttt) cc_final: 0.8287 (mptt)
REVERT: B   59 LYS cc_start: 0.8382 (tttt) cc_final: 0.7850 (tmtt)
REVERT: B   82 THR cc_start: 0.8533 (t) cc_final: 0.8169 (m)
REVERT: B   88 TYR cc_start: 0.7789 (m-10) cc_final: 0.7373 (m-10)
REVERT: D   48 ASP cc_start: 0.8093 (p0) cc_final: 0.7801 (p0)
REVERT: D   77 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8484 (tp)
REVERT: E   49 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.6189 (tpm170)
REVERT: F   88 TYR cc_start: 0.8563 (m-80) cc_final: 0.8126 (m-80)
REVERT: H   39 TYR cc_start: 0.7794 (t80) cc_final: 0.7438 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 169
  average time/residue: 0.1219
  time to fit residues: 28.0246
Evaluate side-chains
  165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9990
   chunk 96 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.136262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.112469 restraints weight = 24234.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.114317 restraints weight = 14534.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.115471 restraints weight = 10548.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.116233 restraints weight = 8779.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.116623 restraints weight = 7901.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12736  Z= 0.145
  Angle     :  0.566   9.181  18461  Z= 0.329
  Chirality :  0.033   0.146   2098
  Planarity :  0.004   0.052   1318
  Dihedral  : 30.000 156.011   4040
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.57 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.32), residues: 728
  helix: -0.27 (0.25), residues: 466
  sheet:  None (None), residues: 0
  loop : -1.67 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  76 
 TYR   0.051   0.002   TYR F  88 
 PHE   0.010   0.001   PHE H  67 
 HIS   0.001   0.000   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12736)
  covalent geometry    : angle       0.56636 (18461)
  hydrogen bonds       : bond        0.05153 (  431)
  hydrogen bonds       : angle       2.53148 ( 1038)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8949 (pt) cc_final: 0.8712 (mt)
REVERT: A   73 GLU cc_start: 0.6950 (tt0) cc_final: 0.6609 (tp30)
REVERT: B   31 LYS cc_start: 0.8449 (tttt) cc_final: 0.8243 (mptt)
REVERT: B   35 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7970 (ttp-170)
REVERT: B   82 THR cc_start: 0.8499 (t) cc_final: 0.8072 (m)
REVERT: B   88 TYR cc_start: 0.7661 (m-10) cc_final: 0.7211 (m-10)
REVERT: C   49 TYR cc_start: 0.8471 (t80) cc_final: 0.7967 (t80)
REVERT: D   48 ASP cc_start: 0.8007 (p0) cc_final: 0.7697 (p0)
REVERT: F   88 TYR cc_start: 0.8612 (m-80) cc_final: 0.7926 (m-80)
REVERT: G  103 GLN cc_start: 0.8437 (pt0) cc_final: 0.8168 (pt0)
  outliers start: 16
  outliers final: 11
  residues processed: 175
  average time/residue: 0.1374
  time to fit residues: 32.3933
Evaluate side-chains
  163 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0020
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.9996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.132679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.108725 restraints weight = 24414.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.110508 restraints weight = 14758.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111651 restraints weight = 10766.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.112378 restraints weight = 8975.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.112804 restraints weight = 8084.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12736  Z= 0.190
  Angle     :  0.612   9.857  18461  Z= 0.352
  Chirality :  0.035   0.146   2098
  Planarity :  0.004   0.051   1318
  Dihedral  : 30.236 158.219   4040
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 27.99 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.31), residues: 728
  helix: -0.34 (0.25), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.95 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  76 
 TYR   0.054   0.003   TYR F  88 
 PHE   0.007   0.001   PHE E 104 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (12736)
  covalent geometry    : angle       0.61195 (18461)
  hydrogen bonds       : bond        0.05541 (  431)
  hydrogen bonds       : angle       2.75725 ( 1038)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7210 (tt0) cc_final: 0.6716 (tp30)
REVERT: B   31 LYS cc_start: 0.8547 (tttt) cc_final: 0.8302 (mptt)
REVERT: B   82 THR cc_start: 0.8563 (t) cc_final: 0.8165 (m)
REVERT: B   88 TYR cc_start: 0.7812 (m-10) cc_final: 0.7322 (m-10)
REVERT: D   48 ASP cc_start: 0.8139 (p0) cc_final: 0.7857 (p0)
REVERT: E   42 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.8025 (ttp80)
REVERT: F   88 TYR cc_start: 0.8642 (m-80) cc_final: 0.8058 (m-80)
REVERT: G  103 GLN cc_start: 0.8562 (pt0) cc_final: 0.8304 (pt0)
REVERT: H   39 TYR cc_start: 0.7818 (t80) cc_final: 0.7520 (t80)
  outliers start: 13
  outliers final: 12
  residues processed: 163
  average time/residue: 0.1232
  time to fit residues: 27.7677
Evaluate side-chains
  162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 95 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.134675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.111427 restraints weight = 24349.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.113235 restraints weight = 14601.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.114437 restraints weight = 10582.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.115149 restraints weight = 8751.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.115507 restraints weight = 7874.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12736  Z= 0.150
  Angle     :  0.581  10.104  18461  Z= 0.336
  Chirality :  0.033   0.140   2098
  Planarity :  0.004   0.052   1318
  Dihedral  : 30.020 157.109   4040
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 27.67 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.32), residues: 728
  helix: -0.08 (0.25), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.49 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  76 
 TYR   0.055   0.002   TYR F  88 
 PHE   0.012   0.001   PHE H  67 
 HIS   0.002   0.000   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12736)
  covalent geometry    : angle       0.58081 (18461)
  hydrogen bonds       : bond        0.05183 (  431)
  hydrogen bonds       : angle       2.55558 ( 1038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1671.19 seconds
wall clock time: 29 minutes 36.24 seconds (1776.24 seconds total)